Oral disease is a major problem in patients with HIV/AIDS. Severe immune suppression due to HIV infection often tends to favor colonization and overgrowth of opportunistic pathogens, which alter the normally balanced oral microflora, contributing to accelerated oral disease. Although more than 700 oral bacterial species have been reported by cultivation and culture-independent molecular methods, recent metagenomic studies suggest that the oral microbial diversity may be up to ten times higher than previously thought. Little is known about the composition, diversity, and evolution of oral polymicrobial communities in HIV- infected individuals, nor the relationships between changes in oral microflora during immunosuppression and the pathogenesis of oral disease. Recent advances in molecular techniques have led to an unprecedented ability to examine deep into the microbial communities, allowing us to begin dissecting the roles of individual species in disease initiation and progression. We have utilized high-density deep sequencing in previous work to identify rare drug resistant mutations in HIV, characterize Hepatitis C virus transmission and diversification, and map retroviral insertion sites in humans genome-wide. Recently we used deep sequencing to characterize subgingival microbiota in children with aggressive periodontitis, identifying many phylotypes not previously recognized as constituents of the oral microbiota. We will take advantage of our experience with deep sequencing and the wealth of clinical resources at the University of Florida and the North Florida/South Georgia VA Medical Center, to characterize the composition, diversity and evolution of oral microbiota in HIV-infected and uninfected individuals with and without periodontal disease, and to define the relationships between alterations in oral microbiota and periodontal disease in the context of host immune status, with the ultimate goal of understanding molecular mechanisms, thereby guiding therapy for periodontal disease. Our hypothesis is that alterations in oral microbiota induce periodontal disease, that immune suppression from HIV accelerates periodontal disease via progressive changes in oral microbiome, and that these dynamic changes are modulated by HAART-related immune reconstitution. We will address these hypotheses using deep sequencing and bioinformatics methods, while contributing high quality oral microbiome data sets to the field via the following Specific Aims: (1) Define the oral microbiomes in HIV infected and uninfected individuals with and without periodontal disease;(2) Determine the impact of HIV immune deficiency and HAART-mediated immune reconstitution on oral microbiomes;(3) Determine the effect of cigarette smoking on oral microbiomes;(4) Define oral archaeal and fungal constituents in HIV+ and HIV- individuals with and without periodontal disease;(5) Characterize the oral metagenomes in periodontal disease.